2ON3

A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 3-aminooxy-1-aminopropane


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5288.1525% PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris, 2 mM APA, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K
Crystal Properties
Matthews coefficientSolvent content
2.1342.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.54α = 90
b = 104.84β = 90
c = 137.35γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-06-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-2MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1319.82271804122
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
33.161000.1330.2897.327.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT319.821625018061000.235870.229610.29254RANDOM31.218
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1-0.89-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.331
r_dihedral_angle_3_deg20.319
r_dihedral_angle_4_deg16.094
r_dihedral_angle_1_deg6.5
r_scangle_it2.625
r_angle_refined_deg1.521
r_scbond_it1.508
r_mcangle_it1.481
r_mcbond_it0.822
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.331
r_dihedral_angle_3_deg20.319
r_dihedral_angle_4_deg16.094
r_dihedral_angle_1_deg6.5
r_scangle_it2.625
r_angle_refined_deg1.521
r_scbond_it1.508
r_mcangle_it1.481
r_mcbond_it0.822
r_nbtor_refined0.323
r_symmetry_vdw_refined0.314
r_nbd_refined0.234
r_symmetry_hbond_refined0.191
r_xyhbond_nbd_refined0.146
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6146
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing